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- PDB-1gnz: LECTIN I-B4 FROM GRIFFONIA SIMPLICIFOLIA (GS I-B4)METAL FREE FORM -

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Basic information

Entry
Database: PDB / ID: 1gnz
TitleLECTIN I-B4 FROM GRIFFONIA SIMPLICIFOLIA (GS I-B4)METAL FREE FORM
ComponentsGSI-B4 ISOLECTIN
KeywordsSUGAR BINDING PROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / GSI-B4 isolectin
Similarity search - Component
Biological speciesGRIFFONIA SIMPLICIFOLIA (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLescar, J. / Loris, R. / Mitchell, E. / Gautier, C. / Imberty, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Isolectins I-A and I-B of Griffonia (Bandeiraea) Simplicifolia. Crystal Structure of Metal-Free Gs I-B(4) and Molecular Basis for Metal Binding and Monosaccharide Specificity.
Authors: Lescar, J. / Loris, R. / Mitchell, E. / Gautier, C. / Chazalet, V. / Cox, V. / Wyns, L. / Perez, S. / Breton, C. / Imberty, A.
History
DepositionOct 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 18, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GSI-B4 ISOLECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9635
Polymers28,3301
Non-polymers6324
Water1,22568
1
A: GSI-B4 ISOLECTIN
hetero molecules

A: GSI-B4 ISOLECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,92510
Polymers56,6602
Non-polymers1,2658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)75.927, 75.927, 190.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-302-

PO4

21A-410-

HOH

31A-465-

HOH

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Components

#1: Protein GSI-B4 ISOLECTIN


Mass: 28330.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: LECTIN I-B4, METAL FREE FORM / Source: (natural) GRIFFONIA SIMPLICIFOLIA (plant) / Organ: SEED / References: UniProt: Q8W1R6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDEPOSITED AS AF428148 IN GENBANK

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris-HCl1reservoirpH8.5
22 Mammonium dihydrogen phosphate1reservoir
35 %water1drop
45 mg/mlGS I-B41drop
50.050 mg/mlalphaGal1-3Gal1drop

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93
DetectorType: QUANTUM CORPORATION / Detector: CCD / Date: Oct 15, 2000 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 11985 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.501 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 4.42 % / Num. measured all: 53046 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / Redundancy: 4.31 % / Num. unique obs: 1144 / Num. measured obs: 4928 / Mean I/σ(I) obs: 3.64

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Processing

Software
NameVersionClassification
CNS1refinement
HKLdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJK

1bjk


Resolution: 2.5→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1100 9 %RANDOM
Rwork0.228 ---
obs0.228 11985 99.7 %-
Solvent computationSolvent model: FLAT / Bsol: 60.78 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 48.38 Å2
Baniso -1Baniso -2Baniso -3
1-10.164 Å20 Å20 Å2
2--10.164 Å20 Å2
3----3.356 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 36 68 1859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008751
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.79541
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.54 Å / Total num. of bins used: 21
RfactorNum. reflection% reflection
Rfree0.3555 49 8.6 %
Rwork0.3201 518 -
obs--98.3 %
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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